Alexei Navalny said on blog that the final tally was "rigged" and demanded a recount.
Russian officials and businessmen have stolen billions of dollars during the years of preparations for the 2014 Winter Games in Sochi.
Vladislav Surkov's ouster followed feud with investigators of innovation project.
Russia is pushing to enforce law requiring all NGOs funded from abroad to register as 'foreign agents.'
Since it began on May 7, Putin's third term in the Kremlin has appeared mostly defensive and downbeat.
